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- PDB-2yni: HIV-1 Reverse Transcriptase in complex with inhibitor GSK952 -

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Basic information

Entry
Database: PDB / ID: 2yni
TitleHIV-1 Reverse Transcriptase in complex with inhibitor GSK952
Components
  • P51 RT
  • REVERSE TRANSCRIPTASE/RIBONUCLEASE H
KeywordsHYDROLASE / NNRTI
Function / homology
Function and homology information


integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus ...integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / viral life cycle / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / Assembly Of The HIV Virion / Budding and maturation of HIV virion / host multivesicular body / protein processing / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / peptidase activity / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / viral translational frameshifting / lipid binding / symbiont entry into host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / DNA binding / zinc ion binding / identical protein binding / membrane
Similarity search - Function
HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. ...HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Nucleotidyltransferase; domain 5 / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / Roll / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-CXD / D(-)-TARTARIC ACID / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHIV-1 M\:B_HXB2R (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsChong, P. / Sebahar, P. / Youngman, M. / Garrido, D. / Zhang, H. / Stewart, E.L. / Nolte, R.T. / Wang, L. / Ferris, R.G. / Edelstein, M. ...Chong, P. / Sebahar, P. / Youngman, M. / Garrido, D. / Zhang, H. / Stewart, E.L. / Nolte, R.T. / Wang, L. / Ferris, R.G. / Edelstein, M. / Weaver, K. / Mathis, A. / Peat, A.
CitationJournal: J.Med.Chem. / Year: 2012
Title: Rational Design of Potent Non-Nucleoside Inhibitors of HIV-1 Reverse Transcriptase.
Authors: Chong, P. / Sebahar, P. / Youngman, M. / Garrido, D. / Zhang, H. / Stewart, E.L. / Nolte, R.T. / Wang, L. / Ferris, R.G. / Edelstein, M. / Weaver, K. / Mathis, A. / Peat, A.
History
DepositionOct 15, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Structure summary
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: REVERSE TRANSCRIPTASE/RIBONUCLEASE H
B: P51 RT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,7485
Polymers117,1342
Non-polymers6143
Water6,810378
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6030 Å2
ΔGint-35 kcal/mol
Surface area44320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.497, 154.577, 156.406
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein REVERSE TRANSCRIPTASE/RIBONUCLEASE H / EXORIBONUCLEASE H / P66 RT


Mass: 64895.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HIV-1 M\:B_HXB2R (virus) / Plasmid: PKK233-2 VARIANT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P04585, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H
#2: Protein P51 RT


Mass: 52238.875 Da / Num. of mol.: 1 / Fragment: RESIDUES 588-1015
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HIV-1 M\:B_HXB2R (virus) / Plasmid: PKK233-2 VARIANT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04585

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Non-polymers , 4 types, 381 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#5: Chemical ChemComp-CXD / 4-chloranyl-N-[[4-chloranyl-3-(3-chloranyl-5-cyano-phenoxy)-2-fluoranyl-phenyl]methyl]-1H-imidazole-5-carboxamide


Mass: 439.655 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H10Cl3FN4O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 58 % / Description: NONE
Crystal growpH: 7.5
Details: 100MM HEPES PH 7.5, 10MM SPERMIDINE, 1.1M SODIUM POTASSIUM TARTRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97934
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 30, 2007 / Details: VERTICALLY FOCUSING MIRROR.
RadiationMonochromator: DCM WITH CRYO-COOLED 1ST CRYSTAL SAGITTALLY BENT 2ND
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.49→40 Å / Num. obs: 50530 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 41.4 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 30.9
Reflection shellResolution: 2.49→2.58 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 4.96 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YNG

2yng


Resolution: 2.49→39.13 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.91 / SU B: 8.656 / SU ML: 0.192 / Cross valid method: THROUGHOUT / ESU R: 0.369 / ESU R Free: 0.263 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2536 1576 3.1 %RANDOM
Rwork0.20214 ---
obs0.2037 48835 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.108 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2---0.98 Å20 Å2
3---0.92 Å2
Refinement stepCycle: LAST / Resolution: 2.49→39.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7815 0 39 378 8232
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.028104
X-RAY DIFFRACTIONr_bond_other_d0.0010.025539
X-RAY DIFFRACTIONr_angle_refined_deg1.0531.96211040
X-RAY DIFFRACTIONr_angle_other_deg0.767313592
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.465967
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.13625.125361
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.675151420
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8551532
X-RAY DIFFRACTIONr_chiral_restr0.0590.21203
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218823
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021557
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.49→2.554 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 109 -
Rwork0.285 3348 -
obs--99.97 %

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